And already a SAM related problem...

[ogs]

I've had the thumping noise in my own system on both SAM1 and SAM2. It is related to deep bass content (below 30Hz or even 20Hz) I recently got my speakers measured for SAM and still had the noise on certain tracks after I enabled the new SAM profile (SAM is always at 100%). It was worse when I played loud(ish). I use room correction so I had to adjust the target curve EQ in the deep bass to get rid of the problem.
I am not suggesting you use the rumble filter on a permanent basis, just temporary until the issue is solved. You need to report this to Devialet so they can look at it and find a fix. I actually mentioned the thumping to Maxime Dumont when he did the SAM measurements on my speaker. He said that it shouldn't be like this. He also told me that SAM does high pass filtering to avoid too much low frequency content passing through SAM.